move doc for update.poisson_reg()

.github/workflows/R-CMD-check.yaml

@@ -1,18 +1,14 @@
-# NOTE: This workflow is overkill for most R packages
-# check-standard.yaml is likely a better choice
-# usethis::use_github_action("check-standard") will install it.
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 #
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -27,62 +23,41 @@ jobs:
       matrix:
         config:
           - {os: macOS-latest,   r: 'release'}
+
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/latest"}
-          - {os: ubuntu-18.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.1.0 (ubuntu-18.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: '3.6',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          # Use 3.6 to trigger usage of RTools35
+          - {os: windows-latest, r: '3.6'}
+
+          # Use older ubuntu to maximise backward compatibility
+          - {os: ubuntu-18.04,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-18.04,   r: 'release'}
+          - {os: ubuntu-18.04,   r: 'oldrel-1'}
+          - {os: ubuntu-18.04,   r: 'oldrel-2'}
 
     env:
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
 
+      - uses: r-lib/actions/setup-pandoc@v1
+
       - uses: r-lib/actions/setup-r@v1
-        id: install-r
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Install pak and query dependencies
-        run: |
-          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
-          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v1
         with:
-          path: |
-            ${{ env.R_LIBS_USER }}/*
-            !${{ env.R_LIBS_USER }}/pak
-          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
-          pak::pkg_system_requirements("textshaping", execute = TRUE)
-          pak::pkg_system_requirements("gert", execute = TRUE)
-        shell: Rscript {0}
-
-      - name: Install dependencies
-        run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("rcmdcheck")
-        shell: Rscript {0}
+          extra-packages: rcmdcheck
 
       - name: Install Miniconda
         run: |
-          Rscript -e "pak::pkg_install('rstudio/reticulate')"
-          Rscript -e "reticulate::install_miniconda()"
+          pak::pkg_install('rstudio/reticulate')
+          reticulate::install_miniconda()
+        shell: Rscript {0}
 
       - name: Find Miniconda on macOS
         if: runner.os == 'macOS'
@@ -94,20 +69,7 @@ jobs:
           tensorflow::install_tensorflow(version='1.14.0')
         shell: Rscript {0}
 
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v1
 
       - name: Show testthat output
         if: always()
@@ -118,10 +80,5 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@main
         with:
-          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
-
-      - name: Don't use tar from old Rtools to store the cache
-        if: ${{ runner.os == 'Windows' && startsWith(steps.install-r.outputs.installed-r-version, '3.6' ) }}
-        shell: bash
-        run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH

.github/workflows/pkgdown.yaml

@@ -1,68 +1,38 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+# Add Config/Needs/website: tidyverse/tidytemplate to DESCRIPTION
 on:
   push:
-    branches:
-      - master
-      - main
+    branches: [main, master]
+    tags: ['*']
   pull_request:
-    branches:
-      - master
-      - main
+    branches: [main, master]
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
-
       - uses: r-lib/actions/setup-pandoc@v1
 
-      - name: System dependencies
-        run: brew install harfbuzz fribidi
-
-      - name: Install pak and query dependencies
-        run: |
-          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
-          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@v1
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("pkgdown", execute = TRUE)
-          pak::pkg_system_requirements("textshaping", execute = TRUE)
-          pak::pkg_system_requirements("gert", execute = TRUE)
-        shell: Rscript {0}
-
-      - name: Install dependencies
-        run: |
-          pak::local_install_dev_deps(upgrade = TRUE, dependencies = c("all", "Config/Needs/website"))
-          pak::pkg_install("pkgdown")
-        shell: Rscript {0}
-
-      - name: Install Miniconda
-        run: |
-          Rscript -e "pak::pkg_install('rstudio/reticulate')"
-          Rscript -e "reticulate::install_miniconda()"
+          use-public-rspm: true
 
-      - name: Find Miniconda on macOS
-        if: runner.os == 'macOS'
-        run: echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: r-lib/pkgdown
+          needs: website
 
-      - name: Install TensorFlow
+      - name: Install Miniconda + TensorFlow
         run: |
+          pak::pkg_install('rstudio/reticulate')
+          reticulate::install_miniconda()
           reticulate::conda_create('r-reticulate', packages = c('python==3.6.9'))
           tensorflow::install_tensorflow(version='1.14.0')
         shell: Rscript {0}
@@ -71,13 +41,13 @@ jobs:
         run: R CMD INSTALL .
 
       - name: Build site
-        if: github.ref != 'refs/heads/master'
+        if: github.event_name == 'pull_request'
         run: |
           Rscript -e 'pkgdown::build_site()'
 
       - name: Deploy package
-        if: github.ref == 'refs/heads/master'
+        if: github.event_name == 'push'
         run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Actions"
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
           Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

.github/workflows/pr-commands.yaml

@@ -1,55 +1,75 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   issue_comment:
     types: [created]
+
 name: Commands
+
 jobs:
   document:
-    if: startsWith(github.event.comment.body, '/document')
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
     name: document
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
+
       - uses: r-lib/actions/pr-fetch@v1
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
+
       - uses: r-lib/actions/setup-r@v1
-      - name: Install dependencies
-        run: Rscript -e 'install.packages(c("remotes", "roxygen2"))' -e 'remotes::install_deps(dependencies = TRUE)'
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: roxygen2
+
       - name: Document
         run: Rscript -e 'roxygen2::roxygenise()'
+
       - name: commit
         run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Actions"
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
           git add man/\* NAMESPACE
           git commit -m 'Document'
+
       - uses: r-lib/actions/pr-push@v1
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
+
   style:
-    if: startsWith(github.event.comment.body, '/style')
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
     name: style
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
+
       - uses: r-lib/actions/pr-fetch@v1
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
+
       - uses: r-lib/actions/setup-r@v1
+
       - name: Install dependencies
         run: Rscript -e 'install.packages("styler")'
+
       - name: Style
         run: Rscript -e 'styler::style_pkg()'
+
       - name: commit
         run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Actions"
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
           git add \*.R
           git commit -m 'Style'
+
       - uses: r-lib/actions/pr-push@v1
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}